qcMWRcom {MassWateR}

Run quality control completeness checks for water quality monitoring results

Description

Run quality control completeness checks for water quality monitoring results

Usage

qcMWRcom(res = NULL, frecom = NULL, fset = NULL, runchk = TRUE, warn = TRUE)

Arguments

res

character string of path to the results file or data.frame for results returned by readMWRresults

frecom

character string of path to the data quality objectives file for frequency and completeness or data.frame returned by readMWRfrecom

fset

optional list of inputs with elements named res, acc, frecom, sit, or wqx overrides the other arguments

runchk

logical to run data checks with checkMWRresults and checkMWRfrecom, applies only if res or frecom are file paths

warn

logical to return warnings to the console (default)

Details

The function can be used with inputs as paths to the relevant files or as data frames returned by readMWRresults and readMWRfrecom. For the former, the full suite of data checks can be evaluated with runkchk = T (default) or suppressed with runchk = F. In the latter case, downstream analyses may not work if data are formatted incorrectly. For convenience, a named list with the input arguments as paths or data frames can be passed to the fset argument instead. See the help file for utilMWRinput.

Note that frequency is only evaluated on parameters in the Parameter column in the data quality objectives frequency and completeness file. A warning is returned if there are parameters in Parameter in the frequency and completeness file that are not in Characteristic Name in the results file.

Similarly, parameters in the results file in the Characteristic Name column that are not found in the data quality objectives frequency and completeness file are not evaluated. A warning is returned if there are parameters in Characteristic Name in the results file that are not in Parameter in the frequency and completeness file.

Value

The output shows the completeness checks from the combined files. Each row applies to a completeness check for a parameter. The datarec and qualrec columns show the number of data records and qualified records, respectively. The datarec column specifically shows only records not for quality control by excluding those as duplicates, blanks, or spikes in the count. The standard column shows the relevant percentage required for the quality control check from the quality control objectives file, the complete column shows the calculated completeness taken from the input data, and the met column shows if the standard was met by comparing if complete is greater than or equal to standard.

Examples

##
# using file paths

# results path
respth <- system.file('extdata/ExampleResults.xlsx', package = 'MassWateR')

# frequency and completeness path
frecompth <- system.file('extdata/ExampleDQOFrequencyCompleteness.xlsx', 
     package = 'MassWateR')

qcMWRcom(res = respth, frecom = frecompth)

##
# using data frames

# results data
resdat <- readMWRresults(respth)

# frequency and completeness data
frecomdat <- readMWRfrecom(frecompth)

qcMWRcom(res = resdat, frecom = frecomdat)